IODS course project

---

About the project

I’m expect to learn how to do Rstudio with huge data. In addition, I want to know about how to visualize the data properly.

Link: https://github.com/swinesci/IODS-project

I have a problem with chapter 2

Write a short description about the course and add a link to your GitHub repository here. This is an R Markdown (.Rmd) file so you can use R Markdown syntax.

---

Excercise 2

to see the data

df <- read.table("http://s3.amazonaws.com/assets.datacamp.com/production/course_2218/datasets/learning2014.txt", sep=",", header=TRUE)

to see structure and dimmension

str(df)

## 'data.frame':    166 obs. of  7 variables:
##  $ gender  : Factor w/ 2 levels "F","M": 1 2 1 2 2 1 2 1 2 1 ...
##  $ age     : int  53 55 49 53 49 38 50 37 37 42 ...
##  $ attitude: num  3.7 3.1 2.5 3.5 3.7 3.8 3.5 2.9 3.8 2.1 ...
##  $ deep    : num  3.58 2.92 3.5 3.5 3.67 ...
##  $ stra    : num  3.38 2.75 3.62 3.12 3.62 ...
##  $ surf    : num  2.58 3.17 2.25 2.25 2.83 ...
##  $ points  : int  25 12 24 10 22 21 21 31 24 26 ...

dim(df)

## [1] 166   7

to acess the ggplot 2 library

library(ggplot2)
ggplot(df)

pairs(df[-1])

## to access the GGally and ggplot2

library(GGally)

## Registered S3 method overwritten by 'GGally':
##   method from   
##   +.gg   ggplot2

library(ggplot2)

to see summary

summary(df)

##  gender       age           attitude          deep            stra      
##  F:110   Min.   :17.00   Min.   :1.400   Min.   :1.583   Min.   :1.250  
##  M: 56   1st Qu.:21.00   1st Qu.:2.600   1st Qu.:3.333   1st Qu.:2.625  
##          Median :22.00   Median :3.200   Median :3.667   Median :3.188  
##          Mean   :25.51   Mean   :3.143   Mean   :3.680   Mean   :3.121  
##          3rd Qu.:27.00   3rd Qu.:3.700   3rd Qu.:4.083   3rd Qu.:3.625  
##          Max.   :55.00   Max.   :5.000   Max.   :4.917   Max.   :5.000  
##       surf           points     
##  Min.   :1.583   Min.   : 7.00  
##  1st Qu.:2.417   1st Qu.:19.00  
##  Median :2.833   Median :23.00  
##  Mean   :2.787   Mean   :22.72  
##  3rd Qu.:3.167   3rd Qu.:27.75  
##  Max.   :4.333   Max.   :33.00

create a more advanced plot matrix with ggpairs

p <- ggpairs(df, maaping = aes(col = gender, alpha = 0.3), lower = list(combo = wrap("facethist", bins = 20)))

## Warning in warn_if_args_exist(list(...)): Extra arguments: "maaping" are
## being ignored. If these are meant to be aesthetics, submit them using the
## 'mapping' variable within ggpairs with ggplot2::aes or ggplot2::aes_string.

to draw the plot

p

##The three explanatory variables are “attitude”, “strategy” and “surface”. These are choosen based on r value

to see scatter plot

qplot(attitude, points, data = df) + geom_smooth(method = "lm")

## fit a linear model

model <- lm(points ~1, data = df)

summary of the model

summary(model)

## 
## Call:
## lm(formula = points ~ 1, data = df)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -15.7169  -3.7169   0.2831   5.0331  10.2831 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  22.7169     0.4575   49.65   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 5.895 on 165 degrees of freedom

to create an plot matrix

library(GGally)
ggpairs(df, lower = list(combo = wrap("facethist", bins = 20)))

to create a regression model with multibple explanatory variables

model2<- lm(points ~ attitude + stra + surf, data = df)
summary(model2)

## 
## Call:
## lm(formula = points ~ attitude + stra + surf, data = df)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -17.1550  -3.4346   0.5156   3.6401  10.8952 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  11.0171     3.6837   2.991  0.00322 ** 
## attitude      3.3952     0.5741   5.913 1.93e-08 ***
## stra          0.8531     0.5416   1.575  0.11716    
## surf         -0.5861     0.8014  -0.731  0.46563    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 5.296 on 162 degrees of freedom
## Multiple R-squared:  0.2074, Adjusted R-squared:  0.1927 
## F-statistic: 14.13 on 3 and 162 DF,  p-value: 3.156e-08

remove the surf because its p value was the highest

model3<- lm(points ~attitude + stra, data=df)
summary(model3)

## 
## Call:
## lm(formula = points ~ attitude + stra, data = df)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -17.6436  -3.3113   0.5575   3.7928  10.9295 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)   8.9729     2.3959   3.745  0.00025 ***
## attitude      3.4658     0.5652   6.132 6.31e-09 ***
## stra          0.9137     0.5345   1.709  0.08927 .  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 5.289 on 163 degrees of freedom
## Multiple R-squared:  0.2048, Adjusted R-squared:  0.1951 
## F-statistic: 20.99 on 2 and 163 DF,  p-value: 7.734e-09

the most significant variable was attitude. Stra had only tendency

to draw diagnostic plots

par(mfrow = c(2,2))
plot(model3, which = c(1,2,5))

QQ plot showed this model is normally distributed all looks good

---

Excercise 3

alc <- read.csv("Z:\\IODS-project\\data\\alc.csv", sep = ",")

access the tidyverse libraries tidyr, dplyr, ggplot2

library(tidyr); library(dplyr); library(ggplot2)

## 
## Attaching package: 'dplyr'

## The following object is masked from 'package:GGally':
## 
##     nasa

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

glimpse at the alc data

glimpse(alc) 

## Observations: 382
## Variables: 36
## $ X          <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, ...
## $ school     <fct> GP, GP, GP, GP, GP, GP, GP, GP, GP, GP, GP, GP, GP,...
## $ sex        <fct> F, F, F, F, F, M, M, F, M, M, F, F, M, M, M, F, F, ...
## $ age        <int> 18, 17, 15, 15, 16, 16, 16, 17, 15, 15, 15, 15, 15,...
## $ address    <fct> U, U, U, U, U, U, U, U, U, U, U, U, U, U, U, U, U, ...
## $ famsize    <fct> GT3, GT3, LE3, GT3, GT3, LE3, LE3, GT3, LE3, GT3, G...
## $ Pstatus    <fct> A, T, T, T, T, T, T, A, A, T, T, T, T, T, A, T, T, ...
## $ Medu       <int> 4, 1, 1, 4, 3, 4, 2, 4, 3, 3, 4, 2, 4, 4, 2, 4, 4, ...
## $ Fedu       <int> 4, 1, 1, 2, 3, 3, 2, 4, 2, 4, 4, 1, 4, 3, 2, 4, 4, ...
## $ Mjob       <fct> at_home, at_home, at_home, health, other, services,...
## $ Fjob       <fct> teacher, other, other, services, other, other, othe...
## $ reason     <fct> course, course, other, home, home, reputation, home...
## $ nursery    <fct> yes, no, yes, yes, yes, yes, yes, yes, yes, yes, ye...
## $ internet   <fct> no, yes, yes, yes, no, yes, yes, no, yes, yes, yes,...
## $ guardian   <fct> mother, father, mother, mother, father, mother, mot...
## $ traveltime <int> 2, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 3, 1, 2, 1, 1, 1, ...
## $ studytime  <int> 2, 2, 2, 3, 2, 2, 2, 2, 2, 2, 2, 3, 1, 2, 3, 1, 3, ...
## $ failures   <int> 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ...
## $ schoolsup  <fct> yes, no, yes, no, no, no, no, yes, no, no, no, no, ...
## $ famsup     <fct> no, yes, no, yes, yes, yes, no, yes, yes, yes, yes,...
## $ paid       <fct> no, no, yes, yes, yes, yes, no, no, yes, yes, yes, ...
## $ activities <fct> no, no, no, yes, no, yes, no, no, no, yes, no, yes,...
## $ higher     <fct> yes, yes, yes, yes, yes, yes, yes, yes, yes, yes, y...
## $ romantic   <fct> no, no, no, yes, no, no, no, no, no, no, no, no, no...
## $ famrel     <int> 4, 5, 4, 3, 4, 5, 4, 4, 4, 5, 3, 5, 4, 5, 4, 4, 3, ...
## $ freetime   <int> 3, 3, 3, 2, 3, 4, 4, 1, 2, 5, 3, 2, 3, 4, 5, 4, 2, ...
## $ goout      <int> 4, 3, 2, 2, 2, 2, 4, 4, 2, 1, 3, 2, 3, 3, 2, 4, 3, ...
## $ Dalc       <int> 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, ...
## $ Walc       <int> 1, 1, 3, 1, 2, 2, 1, 1, 1, 1, 2, 1, 3, 2, 1, 2, 2, ...
## $ health     <int> 3, 3, 3, 5, 5, 5, 3, 1, 1, 5, 2, 4, 5, 3, 3, 2, 2, ...
## $ absences   <int> 5, 3, 8, 1, 2, 8, 0, 4, 0, 0, 1, 2, 1, 1, 0, 5, 8, ...
## $ G1         <int> 2, 7, 10, 14, 8, 14, 12, 8, 16, 13, 12, 10, 13, 11,...
## $ G2         <int> 8, 8, 10, 14, 12, 14, 12, 9, 17, 14, 11, 12, 14, 11...
## $ G3         <int> 8, 8, 11, 14, 12, 14, 12, 10, 18, 14, 12, 12, 13, 1...
## $ alc_use    <dbl> 1.0, 1.0, 2.5, 1.0, 1.5, 1.5, 1.0, 1.0, 1.0, 1.0, 1...
## $ high_use   <lgl> FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FAL...

use gather() to gather columns into key-value pairs and then glimpse() at the resulting data

gather(alc) %>% glimpse

## Warning: attributes are not identical across measure variables;
## they will be dropped

## Observations: 13,752
## Variables: 2
## $ key   <chr> "X", "X", "X", "X", "X", "X", "X", "X", "X", "X", "X", "...
## $ value <chr> "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11",...

draw a bar plot of each variable

gather(alc) %>% ggplot(aes(value)) + facet_wrap("key", scales = "free") + geom_bar()

## Warning: attributes are not identical across measure variables;
## they will be dropped

access the tidyverse libraries dplyr and ggplot2

library(dplyr)

library(ggplot2)

produce summary statistics by group

alc %>% group_by(sex) %>% summarise(count = n())

## # A tibble: 2 x 2
##   sex   count
##   <fct> <int>
## 1 F       198
## 2 M       184

library(ggplot2)

initialize a plot of high_use and G3

g1 <- ggplot(alc, aes(x = high_use, y = G3, col = sex))

define the plot as a boxplot and draw it

g1 + geom_boxplot() + ylab("grade")

initialise a plot of high_use and absences

g2 <- ggplot(alc, aes(x = high_use, y = absences, col = sex))

define the plot as a boxplot and draw it

g2 + geom_boxplot() + ggtitle("Student absences by alcohol consumption and sex")

find the model with glm()

m <- glm(high_use ~ failures + absences + sex, data = alc, family = "binomial")

print out a summary of the model

summary(m)

## 
## Call:
## glm(formula = high_use ~ failures + absences + sex, family = "binomial", 
##     data = alc)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -2.1855  -0.8371  -0.6000   1.1020   2.0209  
## 
## Coefficients:
##             Estimate Std. Error z value Pr(>|z|)    
## (Intercept) -1.90297    0.22626  -8.411  < 2e-16 ***
## failures     0.45082    0.18992   2.374 0.017611 *  
## absences     0.09322    0.02295   4.063 4.85e-05 ***
## sexM         0.94117    0.24200   3.889 0.000101 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 465.68  on 381  degrees of freedom
## Residual deviance: 424.40  on 378  degrees of freedom
## AIC: 432.4
## 
## Number of Fisher Scoring iterations: 4

print out the coefficients of the model

coef(m)

## (Intercept)    failures    absences        sexM 
## -1.90296550  0.45081981  0.09321999  0.94116602

alc and dlyr are available

find the model with glm()

m <- glm(high_use ~ failures + absences + sex, data = alc, family = "binomial")

compute odds ratios (OR)

OR <- coef(m) %>% exp

compute confidence intervals (CI)

CI <- confint(m) %>% exp

## Waiting for profiling to be done...

print out the odds ratios with their confidence intervals

cbind(OR, CI)

##                    OR      2.5 %   97.5 %
## (Intercept) 0.1491257 0.09395441 0.228611
## failures    1.5695984 1.08339644 2.294737
## absences    1.0977032 1.05169654 1.150848
## sexM        2.5629682 1.60381392 4.149405

fit the model

m <- glm(high_use ~ failures + absences + sex, data = alc, family = "binomial")

predict() the probability of high_use

probabilities <- predict(m, type = "response")

add the predicted probabilities to ‘alc’

alc <- mutate(alc, probability = probabilities)

use the probabilities to make a prediction of high_use

alc <- mutate(alc, prediction = probability > 0.5)

see the last ten original classes, predicted probabilities, and class predictions

select(alc, failures, absences, sex, high_use, probability, prediction) %>% tail(10)

##     failures absences sex high_use probability prediction
## 373        1        0   M    FALSE   0.3749639      FALSE
## 374        1        7   M     TRUE   0.5353311       TRUE
## 375        0        1   F    FALSE   0.1406689      FALSE
## 376        0        6   F    FALSE   0.2069112      FALSE
## 377        1        2   F    FALSE   0.2199932      FALSE
## 378        0        2   F    FALSE   0.1523192      FALSE
## 379        2        2   F    FALSE   0.3068503      FALSE
## 380        0        3   F    FALSE   0.1647495      FALSE
## 381        0        4   M     TRUE   0.3568828      FALSE
## 382        0        2   M     TRUE   0.3153209      FALSE

tabulate the target variable versus the predictions

table(high_use = alc$high_use, prediction = alc$prediction)

##         prediction
## high_use FALSE TRUE
##    FALSE   259    9
##    TRUE     84   30

access dplyr and ggplot2

library(dplyr); library(ggplot2)

initialize a plot of ‘high_use’ versus ‘probability’ in ‘alc’

g <- ggplot(alc, aes(x = probability, y = high_use, col = prediction))

define the geom as points and draw the plot

g + geom_point()

tabulate the target variable versus the predictions

table(high_use = alc$high_use, prediction = alc$prediction) %>% prop.table %>% addmargins

##         prediction
## high_use      FALSE       TRUE        Sum
##    FALSE 0.67801047 0.02356021 0.70157068
##    TRUE  0.21989529 0.07853403 0.29842932
##    Sum   0.89790576 0.10209424 1.00000000

the logistic regression model m and dataset alc with predictions are available

define a loss function (average prediction error)

loss_func <- function(class, prob) {
  n_wrong <- abs(class - prob) > 0.5
  mean(n_wrong)
}

call loss_func to compute the average number of wrong predictions in the (training) data

loss_func(class = alc$high_use, prob = alc$probability)

## [1] 0.2434555

the logistic regression model m and dataset alc (with predictions) are available

define a loss function (average prediction error)

loss_func <- function(class, prob) {
  n_wrong <- abs(class - prob) > 0.5
  mean(n_wrong)
}

compute the average number of wrong predictions in the (training) data

loss_func(class = alc$high_use, prob = alc$probability)

## [1] 0.2434555

K-fold cross-validation

library(boot)
cv <- cv.glm(data = alc, cost = loss_func, glmfit = m, K = 10)

average number of wrong predictions in the cross validation

cv$delta[1]

## [1] 0.2460733

---

Excercise 4

access the MASS package

library(MASS)

## 
## Attaching package: 'MASS'

## The following object is masked from 'package:dplyr':
## 
##     select

load the data

data("Boston")

explore the dataset

str(Boston)

## 'data.frame':    506 obs. of  14 variables:
##  $ crim   : num  0.00632 0.02731 0.02729 0.03237 0.06905 ...
##  $ zn     : num  18 0 0 0 0 0 12.5 12.5 12.5 12.5 ...
##  $ indus  : num  2.31 7.07 7.07 2.18 2.18 2.18 7.87 7.87 7.87 7.87 ...
##  $ chas   : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ nox    : num  0.538 0.469 0.469 0.458 0.458 0.458 0.524 0.524 0.524 0.524 ...
##  $ rm     : num  6.58 6.42 7.18 7 7.15 ...
##  $ age    : num  65.2 78.9 61.1 45.8 54.2 58.7 66.6 96.1 100 85.9 ...
##  $ dis    : num  4.09 4.97 4.97 6.06 6.06 ...
##  $ rad    : int  1 2 2 3 3 3 5 5 5 5 ...
##  $ tax    : num  296 242 242 222 222 222 311 311 311 311 ...
##  $ ptratio: num  15.3 17.8 17.8 18.7 18.7 18.7 15.2 15.2 15.2 15.2 ...
##  $ black  : num  397 397 393 395 397 ...
##  $ lstat  : num  4.98 9.14 4.03 2.94 5.33 ...
##  $ medv   : num  24 21.6 34.7 33.4 36.2 28.7 22.9 27.1 16.5 18.9 ...

summary(Boston)

##       crim                zn             indus            chas        
##  Min.   : 0.00632   Min.   :  0.00   Min.   : 0.46   Min.   :0.00000  
##  1st Qu.: 0.08204   1st Qu.:  0.00   1st Qu.: 5.19   1st Qu.:0.00000  
##  Median : 0.25651   Median :  0.00   Median : 9.69   Median :0.00000  
##  Mean   : 3.61352   Mean   : 11.36   Mean   :11.14   Mean   :0.06917  
##  3rd Qu.: 3.67708   3rd Qu.: 12.50   3rd Qu.:18.10   3rd Qu.:0.00000  
##  Max.   :88.97620   Max.   :100.00   Max.   :27.74   Max.   :1.00000  
##       nox               rm             age              dis        
##  Min.   :0.3850   Min.   :3.561   Min.   :  2.90   Min.   : 1.130  
##  1st Qu.:0.4490   1st Qu.:5.886   1st Qu.: 45.02   1st Qu.: 2.100  
##  Median :0.5380   Median :6.208   Median : 77.50   Median : 3.207  
##  Mean   :0.5547   Mean   :6.285   Mean   : 68.57   Mean   : 3.795  
##  3rd Qu.:0.6240   3rd Qu.:6.623   3rd Qu.: 94.08   3rd Qu.: 5.188  
##  Max.   :0.8710   Max.   :8.780   Max.   :100.00   Max.   :12.127  
##       rad              tax           ptratio          black       
##  Min.   : 1.000   Min.   :187.0   Min.   :12.60   Min.   :  0.32  
##  1st Qu.: 4.000   1st Qu.:279.0   1st Qu.:17.40   1st Qu.:375.38  
##  Median : 5.000   Median :330.0   Median :19.05   Median :391.44  
##  Mean   : 9.549   Mean   :408.2   Mean   :18.46   Mean   :356.67  
##  3rd Qu.:24.000   3rd Qu.:666.0   3rd Qu.:20.20   3rd Qu.:396.23  
##  Max.   :24.000   Max.   :711.0   Max.   :22.00   Max.   :396.90  
##      lstat            medv      
##  Min.   : 1.73   Min.   : 5.00  
##  1st Qu.: 6.95   1st Qu.:17.02  
##  Median :11.36   Median :21.20  
##  Mean   :12.65   Mean   :22.53  
##  3rd Qu.:16.95   3rd Qu.:25.00  
##  Max.   :37.97   Max.   :50.00

library(tidyr)
library(corrplot)

## corrplot 0.84 loaded

library(dplyr)

calculate the correlation matrix and round it

cor_matrix<-cor(Boston) %>% round(digits = 2 )

print the correlation matrix

cor_matrix

##          crim    zn indus  chas   nox    rm   age   dis   rad   tax
## crim     1.00 -0.20  0.41 -0.06  0.42 -0.22  0.35 -0.38  0.63  0.58
## zn      -0.20  1.00 -0.53 -0.04 -0.52  0.31 -0.57  0.66 -0.31 -0.31
## indus    0.41 -0.53  1.00  0.06  0.76 -0.39  0.64 -0.71  0.60  0.72
## chas    -0.06 -0.04  0.06  1.00  0.09  0.09  0.09 -0.10 -0.01 -0.04
## nox      0.42 -0.52  0.76  0.09  1.00 -0.30  0.73 -0.77  0.61  0.67
## rm      -0.22  0.31 -0.39  0.09 -0.30  1.00 -0.24  0.21 -0.21 -0.29
## age      0.35 -0.57  0.64  0.09  0.73 -0.24  1.00 -0.75  0.46  0.51
## dis     -0.38  0.66 -0.71 -0.10 -0.77  0.21 -0.75  1.00 -0.49 -0.53
## rad      0.63 -0.31  0.60 -0.01  0.61 -0.21  0.46 -0.49  1.00  0.91
## tax      0.58 -0.31  0.72 -0.04  0.67 -0.29  0.51 -0.53  0.91  1.00
## ptratio  0.29 -0.39  0.38 -0.12  0.19 -0.36  0.26 -0.23  0.46  0.46
## black   -0.39  0.18 -0.36  0.05 -0.38  0.13 -0.27  0.29 -0.44 -0.44
## lstat    0.46 -0.41  0.60 -0.05  0.59 -0.61  0.60 -0.50  0.49  0.54
## medv    -0.39  0.36 -0.48  0.18 -0.43  0.70 -0.38  0.25 -0.38 -0.47
##         ptratio black lstat  medv
## crim       0.29 -0.39  0.46 -0.39
## zn        -0.39  0.18 -0.41  0.36
## indus      0.38 -0.36  0.60 -0.48
## chas      -0.12  0.05 -0.05  0.18
## nox        0.19 -0.38  0.59 -0.43
## rm        -0.36  0.13 -0.61  0.70
## age        0.26 -0.27  0.60 -0.38
## dis       -0.23  0.29 -0.50  0.25
## rad        0.46 -0.44  0.49 -0.38
## tax        0.46 -0.44  0.54 -0.47
## ptratio    1.00 -0.18  0.37 -0.51
## black     -0.18  1.00 -0.37  0.33
## lstat      0.37 -0.37  1.00 -0.74
## medv      -0.51  0.33 -0.74  1.00

visualize the correlation matrix

corrplot(cor_matrix, method="circle", type="upper", cl.pos="b", tl.pos="d", tl.cex = 0.6)

It seems that “dis” is closely related to “age”, “nox”, “indus” and “zn”.

center and standardize variables

boston_scaled <- scale(Boston)

summaries of the scaled variables

summary(boston_scaled)

##       crim                 zn               indus        
##  Min.   :-0.419367   Min.   :-0.48724   Min.   :-1.5563  
##  1st Qu.:-0.410563   1st Qu.:-0.48724   1st Qu.:-0.8668  
##  Median :-0.390280   Median :-0.48724   Median :-0.2109  
##  Mean   : 0.000000   Mean   : 0.00000   Mean   : 0.0000  
##  3rd Qu.: 0.007389   3rd Qu.: 0.04872   3rd Qu.: 1.0150  
##  Max.   : 9.924110   Max.   : 3.80047   Max.   : 2.4202  
##       chas              nox                rm               age         
##  Min.   :-0.2723   Min.   :-1.4644   Min.   :-3.8764   Min.   :-2.3331  
##  1st Qu.:-0.2723   1st Qu.:-0.9121   1st Qu.:-0.5681   1st Qu.:-0.8366  
##  Median :-0.2723   Median :-0.1441   Median :-0.1084   Median : 0.3171  
##  Mean   : 0.0000   Mean   : 0.0000   Mean   : 0.0000   Mean   : 0.0000  
##  3rd Qu.:-0.2723   3rd Qu.: 0.5981   3rd Qu.: 0.4823   3rd Qu.: 0.9059  
##  Max.   : 3.6648   Max.   : 2.7296   Max.   : 3.5515   Max.   : 1.1164  
##       dis               rad               tax             ptratio       
##  Min.   :-1.2658   Min.   :-0.9819   Min.   :-1.3127   Min.   :-2.7047  
##  1st Qu.:-0.8049   1st Qu.:-0.6373   1st Qu.:-0.7668   1st Qu.:-0.4876  
##  Median :-0.2790   Median :-0.5225   Median :-0.4642   Median : 0.2746  
##  Mean   : 0.0000   Mean   : 0.0000   Mean   : 0.0000   Mean   : 0.0000  
##  3rd Qu.: 0.6617   3rd Qu.: 1.6596   3rd Qu.: 1.5294   3rd Qu.: 0.8058  
##  Max.   : 3.9566   Max.   : 1.6596   Max.   : 1.7964   Max.   : 1.6372  
##      black             lstat              medv        
##  Min.   :-3.9033   Min.   :-1.5296   Min.   :-1.9063  
##  1st Qu.: 0.2049   1st Qu.:-0.7986   1st Qu.:-0.5989  
##  Median : 0.3808   Median :-0.1811   Median :-0.1449  
##  Mean   : 0.0000   Mean   : 0.0000   Mean   : 0.0000  
##  3rd Qu.: 0.4332   3rd Qu.: 0.6024   3rd Qu.: 0.2683  
##  Max.   : 0.4406   Max.   : 3.5453   Max.   : 2.9865

class of the boston_scaled object

class(boston_scaled)

## [1] "matrix"

change the object to data frame

boston_scaled <- as.data.frame(boston_scaled)

summary of the scaled crime rate

summary(boston_scaled$crim)

##      Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
## -0.419367 -0.410563 -0.390280  0.000000  0.007389  9.924110

create a quantile vector of crim and print it

bins <- quantile(boston_scaled$crim)

bins

##           0%          25%          50%          75%         100% 
## -0.419366929 -0.410563278 -0.390280295  0.007389247  9.924109610

create a categorical variable ‘crime’

crime <- cut(boston_scaled$crim, breaks = bins, include.lowest = TRUE, labels = c("low", "med_low", "med_high", "high"))

look at the table of the new factor crime

table(crime)

## crime
##      low  med_low med_high     high 
##      127      126      126      127

remove original crim from the dataset

boston_scaled <- dplyr::select(boston_scaled, -crim)

add the new categorical value to scaled data

boston_scaled <- data.frame(boston_scaled, crime)

number of rows in the Boston dataset

n <- nrow(Boston)

choose randomly 80% of the rows

ind <- sample(n,  size = n * 0.8)

create train set

train <- boston_scaled[ind,]

create test set

test <- boston_scaled[-ind,]

save the correct classes from test data

correct_classes <- test$crime

remove the crime variable from test data

test <- dplyr::select(test, -crime)

linear discriminant analysis

lda.fit <- lda(crime ~ ., data = train)

print the lda.fit object

lda.fit

## Call:
## lda(crime ~ ., data = train)
## 
## Prior probabilities of groups:
##       low   med_low  med_high      high 
## 0.2500000 0.2376238 0.2549505 0.2574257 
## 
## Group means:
##                  zn      indus        chas        nox         rm
## low       0.9922333 -0.8922623 -0.11640431 -0.8801959  0.4896534
## med_low  -0.1317173 -0.2440210 -0.06727176 -0.5279207 -0.1117978
## med_high -0.3606902  0.1768170  0.14813795  0.3928992  0.1050394
## high     -0.4872402  1.0170690 -0.08304540  1.0494085 -0.4444232
##                 age        dis        rad        tax    ptratio      black
## low      -0.8742295  0.8429465 -0.6987343 -0.7400287 -0.5273445  0.3806156
## med_low  -0.3499218  0.2670170 -0.5380365 -0.4377601 -0.0540392  0.3147942
## med_high  0.4665505 -0.3802264 -0.4120978 -0.3157051 -0.3584025  0.1070738
## high      0.8395306 -0.8834629  1.6386213  1.5144083  0.7813507 -0.7175028
##                lstat        medv
## low      -0.77609920  0.56581151
## med_low  -0.15861039  0.01919829
## med_high  0.05767885  0.16480594
## high      0.91507811 -0.69138805
## 
## Coefficients of linear discriminants:
##                  LD1         LD2          LD3
## zn       0.076765497  0.72396078 -0.944635619
## indus   -0.002156095 -0.21066596  0.201987705
## chas    -0.094472102 -0.08418137  0.007737457
## nox      0.400664604 -0.71133927 -1.257364295
## rm      -0.114828673 -0.10074533 -0.171309519
## age      0.249253395 -0.41291564 -0.343862940
## dis     -0.077492286 -0.31899473 -0.095356700
## rad      3.229972470  0.83227500 -0.199207309
## tax     -0.035537354  0.07430163  0.650176772
## ptratio  0.101506743  0.06076334 -0.171376548
## black   -0.133878107  0.02833075  0.147830126
## lstat    0.226317262 -0.19848656  0.266771069
## medv     0.192987150 -0.32033402 -0.157167620
## 
## Proportion of trace:
##    LD1    LD2    LD3 
## 0.9504 0.0376 0.0120

the function for lda biplot arrows

lda.arrows <- function(x, myscale = 1, arrow_heads = 0.1, color = "orange", tex = 0.75, choices = c(1,2)){
  heads <- coef(x)
  arrows(x0 = 0, y0 = 0, 
         x1 = myscale * heads[,choices[1]], 
         y1 = myscale * heads[,choices[2]], col=color, length = arrow_heads)
  text(myscale * heads[,choices], labels = row.names(heads), 
       cex = tex, col=color, pos=3)
}

target classes as numeric

classes <- as.numeric(train$crime)

plot the lda results

plot(lda.fit, dimen = 2, col = classes, pch = classes)
lda.arrows(lda.fit, myscale = 1)

predict classes with test data

lda.pred <- predict(lda.fit, newdata = test)

cross tabulate the results

table(correct = correct_classes, predicted = lda.pred$class)

##           predicted
## correct    low med_low med_high high
##   low       14      12        0    0
##   med_low    6      20        4    0
##   med_high   0       8       14    1
##   high       0       0        0   23

load MASS and Boston

library(MASS)
data('Boston')

center and standardize variables

boston_scaled <- scale(Boston)

change the object to data frame from matrix type.

boston_scaled <- as.data.frame(boston_scaled)

Calculate the Euclidean distances between observations.

dist_eu <- dist(boston_scaled)

look at the summary of the distances

summary(dist_eu)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.1343  3.4625  4.8241  4.9111  6.1863 14.3970

K-means clustering

km <-kmeans(boston_scaled, centers = 3)

plot the Boston dataset with clusters

pairs(boston_scaled, col = km$cluster)

Boston dataset is available

set.seed(123)

determine the number of clusters

k_max <- 10

calculate the total within sum of squares

twcss <- sapply(1:k_max, function(k){kmeans(boston_scaled, k)$tot.withinss})

visualize the results

library(ggplot2)

qplot(x = 1:k_max, y = twcss, geom = 'line')

k-means clustering

km <-kmeans(boston_scaled, centers = 2)

plot the Boston dataset with clusters

pairs(boston_scaled, col = km$cluster)

ggpairs

library(GGally)
ggpairs(boston_scaled)

Super bonus

model_predictors <- dplyr::select(train, -crime)

check the dimensions

dim(model_predictors)

## [1] 404  13

dim(lda.fit$scaling)

## [1] 13  3

matrix multiplication

matrix_product <- as.matrix(model_predictors) %*% lda.fit$scaling
matrix_product <- as.data.frame(matrix_product)

library(plotly)

## 
## Attaching package: 'plotly'

## The following object is masked from 'package:MASS':
## 
##     select

## The following object is masked from 'package:ggplot2':
## 
##     last_plot

## The following object is masked from 'package:stats':
## 
##     filter

## The following object is masked from 'package:graphics':
## 
##     layout

3D figure

plot_ly(x = matrix_product$LD1, y = matrix_product$LD2, z = matrix_product$LD3, type= 'scatter3d', mode='markers', color = train$crime )

First one needs to do k-means with 4 clusters to compare the methods.

km3D <-kmeans(boston_scaled, centers = 4)

3D figure

plot_ly(x = matrix_product$LD1, y = matrix_product$LD2, z = matrix_product$LD3, type= 'scatter3d', mode='markers', color = km3D$cluster[ind])

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